[Freesurfer] old colin27
Dear freesurfer I am looking for old segmentation of Colin27 that you have replaced with new version. Is there anywhere that I can find archive of colin27 segmentations. I think it might be segmented with freesurfer 3 or 4. Because I have some labels from the old version. But I dont have the segmentation files and all surfaces. I think I need all surfaces to be able to use label2label command. one surface that I have, shows the lh.pial has 170783 vertices and it could be created in 2010 or before. Could you help me about that? -- Best Regards Rouhollah Abdollahi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] create high resolution ribbon
Dear Freesurfer experts, I tried to create high resolution ribbon from pial and white surfaces. Actually I found this question in mailing list but the answer was not clear. I have a register.dat file and white and pial surfaces. My aim is to create a high resolution ribbon from those by using register.dat. What is the stream line or commands to do that? -- Best Regards Rouhollah Abdollahi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_vol2surf sampling higher resolution
Dear Freesurfer, I have created a ribbon in high resolution like 0.5 x 0.5 x 0.5 mm^3 I selected some of those voxel in the high-res ribbon file. Then I wanted to create a paint file out of volume in that resolution on white or pial. I used the tkregister to register the high-res ribbon file to anatomy. then I used "mri_vol2surf --src seeg_in_ribbon.nii --src_type t1 --srcreg register3.dat --hemi rh --projfrac 1 --out ./seeg_in_ribbon_surface.w --out_type paint --surf pial" to project the volume on surface! but unfortunately I did not get any hits! I already know I should get some vertices but nothing is there!? INFO: output format is paint srcvol = seeg_in_ribbon.nii srctype = t1 srcreg = register3.dat srcregold = 0 srcwarp unspecified surf = pial hemi = rh ProjFrac = 1 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /data/local/PROJECT/subj1/surf/rh.pial Done reading source surface Reading thickness /data/local/PROJECT/subj1/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 1 1 1 using old Done mapping volume to surface Number of source voxels hit = 122086 Warning: all vertex values are zero -- Best Regards Rouhollah Abdollahi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Label2label on fsaverage
Dear freesurfer experts I've tried to export my label file from individual space to fsaverage space by using this command: mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject SUB1 --trglabel rh.V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg sphere.reg --hemi rh and when I tried to load the output label file on fsaverage surface like inflated one it shows a lot of point looks like it is not deformed properly. Is it related to registration to fsaverage or something esle? The question is how I can register the subjects surfaces to fsaverage surfaces? -- With Best Regards Rouhi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Flipping analyze images
Dear Catherine I think freesurfer uses the voxel space not world space (hdr file). some other programs use hdr file too which means world space like spm. if you want to have same world space and voxel space you have to have re-slice your img file in spm if you use spm. then everything would be same in every program. Best Rouhi On Thu, Aug 11, 2011 at 4:34 PM, Catherine Wan wrote: > Dear List, > > I have a question regarding using .img in Freesurfer. > > We only have analyze images, but we can tell the orientation of the images > through the patient's lesion location. Because freesurfer sometimes flips > these image after recon-all, I'm now flipping the "problematic" ones using > mri_convert --out_orientation RAS before running them > again. > > Could someone please explain why if we use analyze images, some of them > would be flipped by Freesurfer but not others? Does that only apply to > lesioned/patient brains and not normal brains? > > Many thanks! > Catherine > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- With Best Regards Rouhollah Abdollahi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Label2label on fsaverage
Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi wrote: > Dear Bruce > > I am working on Freesurfer 2 caret meshes. I am using > FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create > caret surfaces. when I look at my subjects' surfaces I can see in flat map > in caret some of subjects sulci patterns are really distorted and I think it > is related to sphere registration to fsaverage sphere. > Beacsue the code is using sphere.reg to create all surfaces. for the > subjects which I have less distortion on sulci pattern I have good data (3 > subjects) but for the (9 subjects) rest it seems they have problem to > register to fsaverage. Is there any way that I can be sure that > sphere.reg properly created? > > Thank you very much > > Rouhi > > > > On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl > wrote: > >> Try using fsaverage as the trgsubject >> Cheers >> Bruce >> >> >> >> On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi >> wrote: >> >> > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg >> sphere.reg --hemi rh and when I tried to load the output label file on >> fsaverage surface like inflated one it shows a lot of point looks like it is >> not deformed properly. Is it related to registration to fsaverage or >> something esle? The question is how I can register the subjects surfaces to >> fsaverage surfaces? -- With Best Regards Rouhi >> --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable Dear freesurfer experts >> > >> > I've tried to export my label file from individual space to fsaverage >> space by using this command: >> > >> > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject >> SUB1 --trglabel rh.V1_reg. >> > like it is not deformed properly. >> > Is it related to registration to fsaverage or something esle? >> > The question is how I can register the subjects surfaces to fsaverage >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > With Best Regards >Rouhollah Abdollahi > > > > -- With Best Regards Rouhollah Abdollahi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Label2label on fsaverage
Dear Bruce, I have two questions. I saw there are a lot of algorithms for mris_register. Which one are more precise and has less distortion on sulci pattern? In initial alignment if I want to rotate the surface with -rotate [ alpha is (ear to ear) beta(Back to nose) ... ]. Am I right?. and if I want that mris_register does not apply any rigid alignment after initial rotation what I have to do? Thanks Rouhi On Thu, Aug 11, 2011 at 9:25 PM, Bruce Fischl wrote: > What format is the attachment in? > > > > On Aug 11, 2011, at 8:32 PM, Rouhollah Abdollahi > wrote: > > Dear Bruce > I checked the parcellation and look quiet OK. I attached two subjects , > whcih subj_1 shows bad registration to fsaverage and subj_2 shows the good > registration. I attached a file which compare two subjects according to > sphere and sphere.reg. For the subj_1 , it has more figures to see how the > parcellation is. > Thanks in advance > > Best > Rouhi > > On Thu, Aug 11, 2011 at 10:48 AM, Bruce Fischl < > fis...@nmr.mgh.harvard.edu> wrote: > >> Hi Rouhi >> >> check the parcellations. If they are correct then the sphere.reg must be >> pretty accurate. >> >> cheers >> Bruce >> >> On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >>> >>> I am working on Freesurfer 2 caret meshes. I am using ** >>> FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to >>> create caret surfaces. when I look at my subjects' >>> surfaces I can see in flat map in caret some of subjects sulci patterns >>> are really distorted and I think it is related to sphere registration to >>> fsaverage sphere. Beacsue >>> the code is using sphere.reg to create all surfaces. for the subjects >>> which I have less distortion on sulci pattern I have good data (3 subjects) >>> but for the (9 subjects) >>> rest it seems they have problem to register to fsaverage. Is there any >>> way that I can be sure that sphere.reg properly created? >>> >>> Thank you very much >>> >>> Rouhi >>> >>> >>> >>> On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> wrote: >>> Try using fsaverage as the trgsubject >>> Cheers >>> Bruce >>> >>> >>> >>> On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi < >>> roohy...@gmail.com> wrote: >>> >>> > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg >>> sphere.reg --hemi rh and when I tried to load the output label file on >>> fsaverage surface >>> like inflated one it shows a lot of point looks like it is not >>> deformed properly. Is it related to registration to fsaverage or something >>> esle? The question is >>> how I can register the subjects surfaces to fsaverage surfaces? -- >>> With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: >>> text/html; >>> charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear >>> freesurfer experts >>> > >>> > I've tried to export my label file from individual space to >>> fsaverage space by using this command: >>> > >>> > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 >>> --trgsubject SUB1 --trglabel rh.V1_reg. >>> > like it is not deformed properly. >>> > Is it related to registration to fsaverage or something esle? >>> > The question is how I can register the subjects surfaces to fsaverage >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> >>> <http://www.partners.org/complianceline>http://www.partners.org/**complianceline >>> . If the e-mail was sent to you in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >>> >>> >>> >>> -- >>> With Best Regards >>>Rouhollah Abdollahi >>> >>> >>> >>> >>> > > > -- > With Best Regards >Rouhollah Abdollahi > > > > > > -- With Best Regards Rouhollah Abdollahi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Label2label on fsaverage
Dear Bruce I have a data set which I can not create the white surfaces because all of my results are according to white surface. I would like to know is there any way to rotate all surfaces and volumes and labels ... (everything) after finishing recon-all process. like 90 degree around X axis? and apply this rotation to all data set? Best Rouhi On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl wrote: > Hi Rouhi > > I don't really understand. Are you saying you transformed the initial image > before giving it to recon-all? There is a switch to mris_register to > initialize with the tal xform, but we never use it as in pretty extensive > tests it didn't seem to help. mris_register has a very large initial capture > range due to it's global search, so I would be surprised if the initial > orientation was the problem. > > > cheers > Bruce > > > On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: > > Dear Bruce >> I think I found the problem. The problem came from the original >> oriantation of T1 image and I think mris_register could not find it itself >> during >> the recon-all. I added to have initial alignment to inflated and the >> problem solved.( mris_register -curve -inflated ?h.sphere > target> ?h.sphere.reg ) I think it is very important to add it to >> recon-all because if the user doesn't know the real oriantation it might >> make >> such a problem. >> >> Thanks for your quick response. >> >> On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi >> wrote: >> Dear Bruce >> >> I am working on Freesurfer 2 caret meshes. I am using ** >> FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to create >> caret >> surfaces. when I look at my subjects' surfaces I can see in flat map >> in caret some of subjects sulci patterns are really distorted >> and I think it is related to sphere registration to fsaverage sphere. >> Beacsue the code is using sphere.reg to create all surfaces. >> for the subjects which I have less distortion on sulci pattern I have >> good data (3 subjects) but for the (9 subjects) rest it seems >> they have problem to register to fsaverage. Is there any way that I >> can be sure that sphere.reg properly created? >> >> Thank you very much >> >> Rouhi >> >> >> >> On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl >> wrote: >> Try using fsaverage as the trgsubject >> Cheers >> Bruce >> >> >> >> On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi >> wrote: >> >> > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg >> sphere.reg --hemi rh and when I tried to load the output >> label file on fsaverage surface like inflated one it shows a lot of >> point looks like it is not deformed properly. Is it related >> to registration to fsaverage or something esle? The question is how I >> can register the subjects surfaces to fsaverage surfaces? >> -- With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 >> Content-Type: text/html; charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable Dear freesurfer experts >> > >> > I've tried to export my label file from individual space to >> fsaverage space by using this command: >> > >> > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 >> --trgsubject SUB1 --trglabel rh.V1_reg. >> > like it is not deformed properly. >> > Is it related to registration to fsaverage or something esle? >> > The question is how I can register the subjects surfaces to fsaverage >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> >> >> -- >> With Best Regards >>Rouhollah Abdollahi >> >> >> >> >> >> >> -- >> With Best Regards >>Rouhollah Abdollahi >> >> >> >> >> -- With Best Regards Rouhollah Abdollahi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Label2label on fsaverage
Dear Bruce If I want to rotate sucli pattern too if it is the same? On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl wrote: > I guess you could rotate the surfaces, save them, then resample the labels > so that they get the new surface coords and sample them into the volume, > then onto the newly created surfaces. Not sure, we haven't ever had to do > anything like this. > > > On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: > > Dear Bruce >> I think the easiest way is to create all surfaces again but with corrected >> and well aligned brain. The next step for me to create new labels from old >> labels based on white surface (90 degree rotated) to new white surface. >> But >> how? Is there any way to do that? I mean like label2label or surf2surf if >> two surfaces are the same but one of them only rotated?! >> >> Bests >> Rouhi >> >> On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> I don't see how anything would work if it was off by 90deg, but >> I guess you should try it >> >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Because I am using a result from a very old experiment >> that done on wrong direction and the orig.mgz s are not >> oriented according to >> freesurfer template. I cannot creat white because all >> results that I have (label files) are on white surface. >> The only way that I think I need to >> realign all surfaces and volume and apply that rotation on >> my label files. >> >> >> On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl >> wrote: >> not easily. Why would you need to do such a thing? >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> >> I have a data set which I can not create the white >> surfaces because all of my results are according to white >> surface. I would >> like to know is >> there any way to rotate all surfaces and volumes and >> labels ... (everything) after finishing recon-all process. >> like 90 degree >> around X axis? >> and apply this rotation to all data set? >> >> Best >> Rouhi >> >> >> On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl >> wrote: >>Hi Rouhi >> >>I don't really understand. Are you saying you >> transformed the initial image before giving it to >> recon-all? There is a >> switch to >>mris_register to initialize with the tal xform, >> but we never use it as in pretty extensive tests it didn't >> seem to help. >>mris_register has a very large initial capture >> range due to it's global search, so I would be surprised >> if the initial >> orientation >>was the problem. >> >>cheers >>Bruce >> >> >>On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: >> >>Dear Bruce >>I think I found the problem. The problem came >> from the original oriantation of T1 image and I think >> mris_register could >> not >> find it itself during >>the recon-all. I added to have initial alignment >> to inflated and the problem solved.( mris_register -curve >> -inflated >>?h.sphere >target> ?h.sphere.reg ) I think it is very >> important to add it to recon-all because if the user >> doesn't know the real >>oriantation it might make >>such a problem. >> >>Thanks for your quick response. >> >>On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah >> Abdollahi wrote: >> Dear Bruce >> >> I am working on Freesurfer 2 caret meshes. >> I am using **FreeSurfer2CaretConvertAndRegi**sterClean.sh >> from Van Essen lab >> to >>create caret >> surfaces. when I look at my subjects' >> surfaces I can see in flat map in caret some of subjects >> sulci patterns are >> really >>distorted >> a
Re: [Freesurfer] Label2label on fsaverage
I tried to rotate the surface by tksurfer and save it as new file . But when I open the new surface like white it was not rotated. Is there any special thing that I have to do? Best Rouhi On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi wrote: > Dear Bruce > If I want to rotate sucli pattern too if it is the same? > > > > On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl > wrote: > >> I guess you could rotate the surfaces, save them, then resample the labels >> so that they get the new surface coords and sample them into the volume, >> then onto the newly created surfaces. Not sure, we haven't ever had to do >> anything like this. >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >>> I think the easiest way is to create all surfaces again but with >>> corrected >>> and well aligned brain. The next step for me to create new labels from >>> old >>> labels based on white surface (90 degree rotated) to new white surface. >>> But >>> how? Is there any way to do that? I mean like label2label or surf2surf if >>> two surfaces are the same but one of them only rotated?! >>> >>> Bests >>> Rouhi >>> >>> On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu> >>> wrote: >>> I don't see how anything would work if it was off by 90deg, but >>> I guess you should try it >>> >>> >>> >>> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >>> >>> Because I am using a result from a very old experiment >>> that done on wrong direction and the orig.mgz s are not >>> oriented according to >>> freesurfer template. I cannot creat white because all >>> results that I have (label files) are on white surface. >>> The only way that I think I need to >>> realign all surfaces and volume and apply that rotation on >>> my label files. >>> >>> >>> On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl >>> wrote: >>> not easily. Why would you need to do such a thing? >>> >>> >>> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >>> >>> Dear Bruce >>> >>> I have a data set which I can not create the white >>> surfaces because all of my results are according to white >>> surface. I would >>> like to know is >>> there any way to rotate all surfaces and volumes and >>> labels ... (everything) after finishing recon-all process. >>> like 90 degree >>> around X axis? >>> and apply this rotation to all data set? >>> >>> Best >>> Rouhi >>> >>> >>> On Fri, Aug 12, 2011 at 9:17 AM, Bruce Fischl >>> wrote: >>>Hi Rouhi >>> >>>I don't really understand. Are you saying you >>> transformed the initial image before giving it to >>> recon-all? There is a >>> switch to >>>mris_register to initialize with the tal xform, >>> but we never use it as in pretty extensive tests it didn't >>> seem to help. >>>mris_register has a very large initial capture >>> range due to it's global search, so I would be surprised >>> if the initial >>> orientation >>>was the problem. >>> >>>cheers >>>Bruce >>> >>> >>>On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: >>> >>>Dear Bruce >>>I think I found the problem. The problem came >>> from the original oriantation of T1 image and I think >>> mris_register could >>> not >>>find it itself during >>>the recon-all. I added to have initial alignment >>> to inflated and the problem solved.( mris_register -curve >>> -inflated >>>?h.sphere >>target> ?h.sphere.reg ) I think it is very >>> important to add it to recon-all because if the user >>> doesn't know the real >>>oriantation it might make >>>such a problem. >>>
Re: [Freesurfer] Label2label on fsaverage
Hi Bruce I think the aseg is good but only rotated 90 degree. I will try to rotate sphere to see how it will create sphere.reg. On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl wrote: > Hi Matt > > if they were tipped forward 90deg and we didn't detect it I would think > that the aseg would fail catastrophically. Did that happen? > Bruce > > On Fri, 12 Aug 2011, Matt Glasser wrote: > > >> So I thought the issue had been solved, but perhaps not. Bruce, we (i.e. >> David) think the problem with Rouhi?s data is that FreeSurfer did not >> detect that the original images were tipped forward 90 degrees and as a >> result the surface registration failed intermittently (i.e. in some >> subjects it okay, but in others it is not). These data were created with >> a fairly old version of FreeSurfer (Rouhi can give the version number), >> and then a significant amount of manual effort was put into defining some >> retinotopy on the data. Therefore it isn?t really a feasible option to >> just rerun the data with a newer version of FreeSurfer, but we want to >> make use of accurate FreeSurfer surface registration to make group average >> retinotopy results. So the question is how do we go about making sure the >> spheres are initialized to have the correct rigid orientation before >> the registration proceeds. >> >> >> >> Thanks, >> >> >> Matt. >> >> >> >> >> __**__** >> __**______** >> _ >> >> >> From: >> freesurfer-boun...@nmr.mgh.**harvard.edu[mailto: >> freesurfer-bounces@**nmr.mgh.harvard.edu] >> On Behalf Of Rouhollah Abdollahi >> Sent: Friday, August 12, 2011 12:38 PM >> To: Bruce Fischl >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Label2label on fsaverage >> >> >> >> I tried to rotate the surface by tksurfer and save it as new file . But >> when I open the new surface like white it was not rotated. >> Is there any special thing that I have to do? >> >> Best >> Rouhi >> >> On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi >> wrote: >> >> Dear Bruce >> If I want to rotate sucli pattern too if it is the same? >> >> >> >> >> On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl >> wrote: >> >> I guess you could rotate the surfaces, save them, then resample the labels >> so that they get the new surface coords and sample them into the >> volume, then onto the newly created surfaces. Not sure, we haven't ever >> had to do anything like this. >> >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> I think the easiest way is to create all surfaces again but with corrected >> and well aligned brain. The next step for me to create new labels from old >> labels based on white surface (90 degree rotated) to new white surface. >> But >> how? Is there any way to do that? I mean like label2label or surf2surf if >> two surfaces are the same but one of them only rotated?! >> >> Bests >> Rouhi >> >> On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> I don't see how anything would work if it was off by 90deg, but >> I guess you should try it >> >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Because I am using a result from a very old experiment >> that done on wrong direction and the orig.mgz s are not >> oriented according to >> freesurfer template. I cannot creat white because all >> results that I have (label files) are on white surface. >> The only way that I think I need to >> realign all surfaces and volume and apply that rotation on >> my label files. >> >> >> On Fri, Aug 12, 2011 at 11:42 AM, Bruce Fischl >> wrote: >> not easily. Why would you need to do such a thing? >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> >> I have a data set which I can not create the white >> surfaces because all of my results are according to white >> surface. I would >> like to know is >> there any way to rotate all surfaces and volumes and >> labels ... (everything) after finishing recon-all process. >>
Re: [Freesurfer] Label2label on fsaverage
where can I upload one subject? which I have problem with that subject in RH registraton. On Sat, Aug 13, 2011 at 10:30 PM, Bruce Fischl wrote: > if the aseg is good I don't see how it's possible that we don't know about > the 90 deg rotation. If you upload the dataset I'll take a look > On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote: > > Hi BruceI think the aseg is good but only rotated 90 degree. I will try >> to rotate sphere to see how it will create sphere.reg. >> >> >> >> On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl >> wrote: >> Hi Matt >> >> if they were tipped forward 90deg and we didn't detect it I would >> think that the aseg would fail catastrophically. Did that happen? >> Bruce >> >> On Fri, 12 Aug 2011, Matt Glasser wrote: >> >> >> So I thought the issue had been solved, but perhaps not. Bruce, we >> (i.e. David) think the problem with Rouhi?s data is that FreeSurfer >> did not >> detect that the original images were tipped forward 90 degrees and as >> a result the surface registration failed intermittently (i.e. in >> some >> subjects it okay, but in others it is not). These data were created >> with a fairly old version of FreeSurfer (Rouhi can give the version >> number), >> and then a significant amount of manual effort was put into defining >> some retinotopy on the data. Therefore it isn?t really a feasible >> option to >> just rerun the data with a newer version of FreeSurfer, but we want >> to make use of accurate FreeSurfer surface registration to make group >> average >> retinotopy results. So the question is how do we go about making >> sure the spheres are initialized to have the correct rigid orientation >> before >> the registration proceeds. >> >> >> >> Thanks, >> >> >> Matt. >> >> >> >> >> __**__** >> __**__** >> _ >> >> >> From: >> freesurfer-boun...@nmr.mgh.**harvard.edu[mailto: >> freesurfer-bounces@**nmr.mgh.harvard.edu] >> On Behalf Of Rouhollah Abdollahi >> Sent: Friday, August 12, 2011 12:38 PM >> To: Bruce Fischl >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Label2label on fsaverage >> >> >> >> I tried to rotate the surface by tksurfer and save it as new file . >> But when I open the new surface like white it was not rotated. >> Is there any special thing that I have to do? >> >> Best >> Rouhi >> >> On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi < >> roohy...@gmail.com> wrote: >> >> Dear Bruce >> If I want to rotate sucli pattern too if it is the same? >> >> >> >> >> On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> >> I guess you could rotate the surfaces, save them, then resample the >> labels so that they get the new surface coords and sample them into >> the >> volume, then onto the newly created surfaces. Not sure, we haven't >> ever had to do anything like this. >> >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> I think the easiest way is to create all surfaces again but with >> corrected >> and well aligned brain. The next step for me to create new labels >> from old >> labels based on white surface (90 degree rotated) to new white >> surface. But >> how? Is there any way to do that? I mean like label2label or >> surf2surf if >> two surfaces are the same but one of them only rotated?! >> >> Bests >> Rouhi >> >> On Fri, Aug 12, 2011 at 12:00 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> I don't see how anything would work if it was off by 90deg, but >> I guess you should try it >> >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Because I am using a result from a very old experiment >> that done on wrong direction and the orig.mgz s are not >> oriented according to >> freesurfer template. I cannot creat white because all >>
Re: [Freesurfer] Label2label on fsaverage
Hi Bruce, My problem has been solved. I rotate the ?h.sphere by mris_rotate 0 0 90 and then I used mris_register to register it to fsaverage and I saw my result is perfectly registered to fsaverage. it means that mris_register was not able to realign the sphere to fsaverage if the original orientation is bigger than some degrees like 90. I don't think you need to spend time on it. thanks alot for your helps. bests Rouhi On Sat, Aug 13, 2011 at 11:09 PM, Bruce Fischl wrote: > you can either ftp it or put it on our file drop (you can find both on our > wiki) > > On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote: > > where can I upload one subject? which I have problem with that subject in >> RH registraton. >> >> On Sat, Aug 13, 2011 at 10:30 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> if the aseg is good I don't see how it's possible that we don't know >> about the 90 deg rotation. If you upload the dataset I'll take a look >> On Sat, 13 Aug 2011, Rouhollah Abdollahi wrote: >> >>Hi BruceI think the aseg is good but only rotated 90 degree. I >> will try to rotate sphere to see how it will create sphere.reg. >> >> >> >> On Sat, Aug 13, 2011 at 1:02 AM, Bruce Fischl >> wrote: >> Hi Matt >> >> if they were tipped forward 90deg and we didn't detect it I would >> think that the aseg would fail catastrophically. Did that happen? >> Bruce >> >> On Fri, 12 Aug 2011, Matt Glasser wrote: >> >> >> So I thought the issue had been solved, but perhaps not. Bruce, we >> (i.e. David) think the problem with Rouhi?s data is that FreeSurfer >> did not >> detect that the original images were tipped forward 90 degrees and as >> a result the surface registration failed intermittently (i.e. in >> some >> subjects it okay, but in others it is not). These data were created >> with a fairly old version of FreeSurfer (Rouhi can give the version >> number), >> and then a significant amount of manual effort was put into defining >> some retinotopy on the data. Therefore it isn?t really a feasible >> option to >> just rerun the data with a newer version of FreeSurfer, but we want >> to make use of accurate FreeSurfer surface registration to make group >> average >> retinotopy results. So the question is how do we go about making >> sure the spheres are initialized to have the correct rigid orientation >> before >> the registration proceeds. >> >> >> >> Thanks, >> >> >> Matt. >> >> >> >> >> >> _**__** >> __**__** >> __ >> >> >> From: >> freesurfer-boun...@nmr.mgh.**harvard.edu[mailto: >> freesurfer-bounces@**nmr.mgh.harvard.edu] >> On Behalf Of Rouhollah Abdollahi >> Sent: Friday, August 12, 2011 12:38 PM >> To: Bruce Fischl >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Label2label on fsaverage >> >> >> >> I tried to rotate the surface by tksurfer and save it as new file . >> But when I open the new surface like white it was not rotated. >> Is there any special thing that I have to do? >> >> Best >> Rouhi >> >> On Fri, Aug 12, 2011 at 2:24 PM, Rouhollah Abdollahi < >> roohy...@gmail.com> wrote: >> >> Dear Bruce >> If I want to rotate sucli pattern too if it is the same? >> >> >> >> >> On Fri, Aug 12, 2011 at 1:10 PM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> >> I guess you could rotate the surfaces, save them, then resample the >> labels so that they get the new surface coords and sample them into >> the >> volume, then onto the newly created surfaces. Not sure, we haven't >> ever had to do anything like this. >> >> >> >> On Fri, 12 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >> I think the easiest way is to create all surfaces again but with >> corrected >> and well aligned brain. The next step for me to create new labels >> from old >> labels based on white surface (90 degree rotated) to new white >> surface. But >> how? Is there any way to do that? I mean like label2label or >> surf2surf if >
Re: [Freesurfer] recon-all error with nu_correct
check this!!! /bin/mv: cannot move `./tmp.mri_nu_correct.mni.26621/1/nu2_residue.mnc' to `./ tmp.mri_nu_correct.mni.26621/1/nu2_est.mnc': Permission denied On Mon, Aug 15, 2011 at 6:03 PM, Ahmed, F, Me < fah...@sun.ac.za> wrote: > Hi Louis, > > The command line I am using at the beginning was the following: > > recon-all-i > NN_117_10/NN117_10.MR.RESEARCH_STELLENBOSCH.2.1.2010.02.09.13.10.21.390625.46080549.IMA > -s NN_117_10 -force -autorecon-all > > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Louis Nicholas Vinke > Sent: 15 August 2011 17:59 > To: Ahmed, F, Me > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all error with nu_correct > > Hi Fatima, > What is the recon-all command line you are using to start the recon? > -Louis > > On Mon, 15 Aug 2011, Ahmed, F, Me wrote: > > > Hello Freesurfer experts, > > > > I am having great difficulty in trying to run the recon-all process on > some scans of mine. I have tried running it a number of times, to no avail > and the error I have gotten most recently is the nu_correct error. I have > attached the log for this recon-all and hope someone may be able to help. > > > > Also, I was told that there is a way one can upload a particular scan via > FTP, is this correct and if so, how does one go about doing this? > > > > Thank you! > > Fatima > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- With Best Regards Rouhollah Abdollahi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
